moldesign.widgets package

moldesign.widgets.configure()[source]
moldesign.widgets.about()

Submodules

moldesign.widgets.computeconfig module

class moldesign.widgets.computeconfig.ChangeLog[source]

Bases: ipywidgets.widgets.widget_box.Box

static version_check()[source]

References

http://code.activestate.com/recipes/577708-check-for-package-updates-on-pypi-works-best-in-pi/

class moldesign.widgets.computeconfig.ComputeConfig[source]

Bases: ipywidgets.widgets.widget_box.Box

apply_config(*args)[source]
reset_config(*args)[source]

Reset configuration in UI widget to the stored values

save_config(*args)[source]
test_connection(*args)[source]
update_engine_display(*args)[source]
class moldesign.widgets.computeconfig.MDTConfig[source]

Bases: ipywidgets.widgets.widget_box.Box

make_header()[source]
class moldesign.widgets.computeconfig.RegistryConfig[source]

Bases: ipywidgets.widgets.widget_box.Box

apply_config(*args)[source]
reset_config(*args)[source]
moldesign.widgets.computeconfig.about()
moldesign.widgets.computeconfig.configure()[source]

moldesign.widgets.configurator module

class moldesign.widgets.configurator.Configurator(paramlist, paramdefs, title=None)[source]

Bases: ipywidgets.widgets.widget_box.Box

Interactive configuration widget for a list of parameters

Parameters:
  • paramlist (Mapping[str,object]) – Mapping of parameter names to their current values
  • paramdefs (Mapping[str,Parameter]) – Mapping of parameter names to their definitions
selectors

Mapping[str,ParamSelector] – Mapping of parameters names to their selector widgets

apply_values(*args)[source]
reset_values(*args)[source]
show_relevant_fields()[source]

moldesign.widgets.geombuilder module

class moldesign.widgets.geombuilder.GeometryBuilder(mol)[source]

Bases: moldesign.uibase.components.ViewerToolBase

DEGFMT = u'{:.1f}\xb0'
HIGHLIGHTOPACITY = 0.6
MAXDIST = 20.0
NBR1HIGHLIGHT = '#AFC6A8'
NBR2HIGHLIGHT = '#C5AED8'
POSFMT = u'{:.3f} \u212b'
VIEWERTYPE

alias of BondClicker

atom_click(atom)[source]
bond_click(bond)[source]
clear_selection(render=True, *args)[source]
label_atoms(*args)[source]
reset_geometry(*args)[source]
set_angle(*args)[source]
set_atom_x(*args)[source]
set_atom_y(*args)[source]
set_atom_z(*args)[source]
set_dihedral(*args)[source]
set_distance(*args)[source]

moldesign.widgets.orbitals module

class moldesign.widgets.orbitals.OrbitalUIPane(viz, **kwargs)[source]

Bases: moldesign.uibase.selector.Selector, ipywidgets.widgets.widget_box.Box

change_resolution(*args)[source]
handle_selection_event(*args)[source]
new_orb_type(*args)[source]

Create list of available orbitals when user selects a new type

new_orbital_selection(*args)[source]
class moldesign.widgets.orbitals.OrbitalViewer(mol, **kwargs)[source]

Bases: moldesign.uibase.selector.SelectionGroup

moldesign.widgets.parameterization module

This module contains methods to display 3D information about the assignment of force field parameters to a biomolecule.

This helps users to visualize errors that occur when trying to assign a forcefield, such as unrecognized residues, missing atoms, etc.

Note

This is currently tied to ambertools and tleap! It will need to be made generic if/when another method for assigning forcefields is added.

class moldesign.widgets.parameterization.ForceFieldMessage[source]

Bases: object

class moldesign.widgets.parameterization.MissingAtom(message, residue, atom)[source]

Bases: moldesign.widgets.parameterization.ForceFieldMessage

show(viewer)[source]
unshow(viewer)[source]
class moldesign.widgets.parameterization.ParameterizationDisplay(errormessages, molin, molout=None)[source]

Bases: ipywidgets.widgets.widget_box.Box

switch_display(d)[source]
class moldesign.widgets.parameterization.UnknownAtom(message, residue, atom)[source]

Bases: moldesign.widgets.parameterization.ForceFieldMessage

show(viewer)[source]
unshow(viewer)[source]
class moldesign.widgets.parameterization.UnknownResidue(message, residue)[source]

Bases: moldesign.widgets.parameterization.ForceFieldMessage

show(viewer)[source]
unshow(viewer)[source]
class moldesign.widgets.parameterization.UnusualBond(message, atoms, residues)[source]

Bases: moldesign.widgets.parameterization.ForceFieldMessage

show(viewer)[source]
unshow(viewer)[source]

moldesign.widgets.selection module

class moldesign.widgets.selection.BondSelector(mol)[source]

Bases: moldesign.uibase.components.SelBase

VIEWERTYPE

alias of BondClicker

static bondkey(bond)[source]
clear_selections(*args)[source]
handle_remove_button_click(*args)[source]
remove_bondlist_highlight(*args)[source]
select_all_bonds(*args)[source]
selected_bonds
toggle_bond(bond)[source]
class moldesign.widgets.selection.ResidueSelector(mol)[source]

Bases: moldesign.uibase.components.SelBase

Selections at the atom/residue/chain level. Selecting a residue selects all of its atoms. Selecting all atoms of a residue is equivalent to selecting the residue. A residue is not selected if only some of its atoms are selected.

atom_click(atom)[source]
static atomkey(atom)[source]
handle_remove_button_click(*args)[source]
remove_reslist_highlight(*args)[source]
static reskey(residue)[source]
selected_residues
toggle_residue(residue, clickatom=None, render=True)[source]

moldesign.widgets.symmetry module

class moldesign.widgets.symmetry.Symmetrizer(mol)[source]

Bases: ipywidgets.widgets.widget_box.Box

apply_selected_symmetry(*args)[source]
coords_changed(*args)[source]
reset_coords(*args)[source]
set_highest_symmetry(*args)[source]
show_symmetry(*args)[source]
viewer = None

type viewer – moldesign.viewer.GeometryViewer

moldesign.widgets.trajectory module

class moldesign.widgets.trajectory.FrameInspector(traj, **kwargs)[source]

Bases: ipywidgets.widgets.widget_string.HTML, moldesign.uibase.selector.Selector

handle_selection_event(selection)[source]
class moldesign.widgets.trajectory.TrajectoryOrbViewer(trajectory, display=False, **kwargs)[source]

Bases: moldesign.widgets.trajectory.TrajectoryViewer

make_viewer()[source]
class moldesign.widgets.trajectory.TrajectoryViewer(trajectory, display=False, **kwargs)[source]

Bases: moldesign.uibase.selector.SelectionGroup

3D representation, with animation controls, for a trajectory.

Users will typically instantiate this using trajectory.draw()

Parameters:
  • display (bool) – immediately display this to the notebook (default: False)
  • **kwargs (dict) – keyword arguments for ipywidgets.Box
animate(fps=None)[source]
make_controls()[source]
make_viewer()[source]